The Real Truth
by EndlessGhostfire
Summary: MUTANT AU - For a while now, John has wondered if Sherlock is the human he claims to be. The truth is soon revealed by a surprise turn of events that change the two men's lives forever. [Eventual Johnlock, Rated M for smut in later chapters and violence]
1. Chapter 1

**Hello, my fellow shippers. First Johnlock story, whoop whoop. It's an AU, which just so happens to be my specialty. This story is set in the Marvel Mutant Universe, exciting, huh?**

**Warnings (why are they called warnings? It's why you read it) : Eventual!Johnlock, Mutant!Sherlock, A bit of violence in later chapters, A bit of angst (but who doesn't love a bit of angst every once and a while?) and, if you're all good and Review, smut in the later chapters.**

**Disclaimer: Don't own anything apart from the plot. Although I wish I could own Sherlock *flails***

**I must also tell you, my right hand is in a cast atm, I have a suspected fractured hand. Sex sent me to the ER, eh, ha ha, but no seriously, my typing skills are very limited at the moment so I apologize if I am slow in updating.**

**Anyway, enjoy peeps!**

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><p>CH 110

Click.

"Get down!" Sherlock shouted to his shorter friend as he leaped out of the way of the thrown grenade.

John quickly followed suit, throwing himself inbetween two of the many shipping containers in the docks, covering his ears and waiting for the explosion.

It never came.

John was about to get up, when he felt a hand on his shoulder. It was Sherlock. "Stay down" He breathed, "It's a dummy grenade, they are ready to shoot when we reappear"

"How do you-"John hissed as Sherlock rolled his eyes and interrupted.

"Not the time, John. We need to get out of here, Lestrade just called the backup to come in"

John stared at his ridiculous friend in disbelief, before being snapped back to the present by the sound of sirens.  
>Sherlock jumped up, grabbing John and hauling him to his feet before taking off at a run directly towards the back-up cars, hearing the clatter of guns start behind them. Once they were behind the safety of one of the cars, Sherlock immediately spoke up.<p>

"Some of them are mutants, all with low level powers but can still be dangerous"

One of the police officers listening nodded and began relaying the information to everyone else and, within half an hour, the drug smugglers had been taken down and Sherlock and John were in –much to the detective's annoyance- Mycroft's car getting told off like a pair of school kids.

"How could you be so stupid, Sherlock?!" Mycroft was stressing at his little brother, who was by the open window, a lit cigarette between his lips – only being used to annoy Mycroft- and was doing his best to ignore him. "You had no idea how many mutants were in that gang, you could have been killed"

"But I wasn't" Sherlock argued, finally deciding to talk. He took a drag of his cigarette and deliberately blew the smoke into Mycroft's face as John tried his best not to laugh.

"This isn't funny, Sherlock" Mycroft said, after he'd recovered, to the smirking detective. "I told you specifically not to go into there alone because they were dangerous and you went against my orders"

"Like Sherlock ever listened to you anyway" John muttered with a chuckle, but quickly sobered up at the glare Mycroft threw his way, "Sorry"

Mycroft sniffed and looked between the two men, "It seems you both are blind to the seriousness of the situation" He said as the car stopped outside 221. "At least you weren't shot, or worse, kidnapped. Now go"

John scoffed, "Alright, Hermione" He muttered under his breath as he exited the car, making Sherlock chuckle.

They unlocked the door and walked up the stairs to their living room in comfortable silence. A nod was the only thing needed to let John know Sherlock wanted tea and went to put the kettle on. Sherlock settled in his chair, putting his hands together under his chin. It was their norm.

That was until John decided to break the silence.

"How did you know that was a dummy grenade back there?" He asked, walking over and leaning on the back of his chair, awaiting his friend's answer.

Sherlock immediately froze. To anyone else but John, Sherlock looked unresponsive, but to John, Sherlock was internally panicking.

It took the detective a few seconds to respond. He cleared his throat and looked away, "Simple observation. It was obviously a dummy"

John didn't believe a word, "You forget, Sherlock, that I served in Afghanistan and know the difference between a real and dummy grenade. You couldn't have known that fast. You hardly looked at the thing"

"Well, I must not be as blind as you"

"Sherlock" John sighed, looking down momentarily, cooling his growing annoyance, "Don't treat me like I'm stupid-"

"You ar-"

"Stop it" John said, using his military voice knowing it would shut his best friend up.

It worked for 10 seconds.

"I just knew it was a dummy. I don't have to explain myself to you, John"

"That's the thing" John replied in disbelief, "You always have to explain yourself, but when I ask a simple innocent question, you become defensive!"

Sherlock pressed his lips into a pout and John knew exactly where this was going.

"Don't you dare go all stroppy on me"

"I'm not in a strop, John"

"Oh, please. You're basically a 16-year-old teenager being denied to go to a party by their parents"

Sherlock shuffled in his seat, crossing his arms over his chest. "Not in a strop" he muttered and John knew that that were the last words he'd get out of Sherlock that night.

The doctor couldn't believe how Sherlock could go from a professional, emotionless detective to a stroppy, hormone fueled teenager in the space of 30 seconds.

Sighing as Sherlock curled more into himself, John walked over to the door and grabbed his coat, making for the dark streets of London to cool his temper.


	2. Chapter 2

CH 2/10

John had been living with the infuriating detective for almost four years, and as John trudged down the streetlamp-lit streets, he wandered how he still had the strength to put up with the self-centred, patronising, adorable idiot.

Ah. That might be it.

For a while now, John had known his feelings towards Sherlock were a lot more than platonic, but would never say anything. God no. He knew how Sherlock felt about relationships and did not want to lose the friendship the two had. So, for as long as he could remember, John vented his frustration by going on dead end dates, and if the girls he dated happened to be tall, blue-eyed and dark haired…well, then so be it.

John sighed, a puff of steam billowing from his mouth into the cold night air. "Yeah" He scoffed, "Not gay, my arse" He muttered to himself.

"Talking to yourself is a sign of madness, you know" A voice suddenly said behind him, making John jump around, his hand instinctively reaching for his Sig he had tucked into the waistband of his jeans. Seeing his grey-haired friend chuckle and raise his hands in surrender made John instantly relax.

"Jesus, Greg, don't startle me like that"

"My fault, I should have known better than to sneak up on an ex-soldier"

John chuckled, "Well, yeah. What are you doing out so late?"

Greg shrugged, "Paperwork at the Yard. Anderson's driving me crazy, so I escaped for a coffee and a ciggy" He said, pulling a box of Marlboro's from his pocket and popping one between his lips.

John raised an eyebrow, "Those things will kill you, you know…but god I need one after the day I've had. Gimme."

Greg smiled as he lit the cigarette, then handed it to John and lit another for himself.

"So…" Greg blew smoke into the night air, "..Fight with the boyfriend?" He looked sideways at his friend, smirking.

John rolled his eyes, deciding not to correct him, "Sometimes he's a complete idiot" He sighed.

"That's true" Greg laughed.

"He is always so defensive if I ask him about how he just knows some things. Sometimes, they seem too impossible for him to deduce"

"Hm. To him, it's almost natural to not talk about those things"

John frowned, "What do you mean?"

Greg took a last drag of his cigarette and flicked it onto the pavement, stubbing it out with his shoe. "Come on, let's find a café that'll serve us at this time and I'll explain"

Half an hour and a mug of coffee later, John and Greg sat in a 24-hour cafe, each nursing their second Mocha of the night and complaining about their first world problems.

John sipped the steaming liquid, enjoying the warmth as it slid down his throat. "So, you were going to explain about Sherlock?" In all honesty, John felt bad about Greg telling him about his best friend's past, but he knew full well that Sherlock would never give him any answers.

Greg nodded, warming his hands on his mug. "Yeah, well, as you probably guessed, Sherlock didn't have the best childhood. Granted, he had a loving mother and father, but he was badly bullied in every school he attended because of his…abilities. It got worse when he went to secondary school and…when he was 18, he was violently attacked, all because he was different to everyone else."

John's heart constricted. He wasn't sure he wanted to hear this, but Greg continued regardless.

"He was left in an alley with two broken ribs, a broken collarbone, a fractured eye socket and minor internal bleeding"

John inhaled sharply, tightening his grip on his mug. Oh, Sherlock…Greg had to take a few breathes before he could continue.

"When he recovered, he hated his abilities and drowned them in drugs. That's when I met him. Even when he was high as a kite, he couldn't help but use his abilities, he was unable to shut them off, no matter how hard he tried. It took a year for me and Mycroft to finally get him sober, and he's stayed sober ever since. In the years I've known him, his abilities have only grown…he truly is a remarkable man." Greg finished and there was a long silence. John was thankful that Greg gave him time to process everything. It was a lot to take in.

About two minutes later, John cleared his throat and downed the rest of his mocha. "Wow…" He muttered as Greg nodded. "You kept saying 'abilities', I'm assuming you mean his power of deduction?"

Greg gave the doctor a knowing smile, which made John frown in confusion. "You'll have to ask Sherlock about that, mate" He answered, finishing his drink and standing up, "Alright, I'd better be off. God knows what state the Yard is in" And with that, John was left alone in the café.

John grumbled. Greg had been spending too much time with Mycroft, he'd become too smug for his own good. Checking his watch, John realized it was well past midnight and began to make his way home.

He got home in less than ten minutes and quietly climbed the stairs as to not wake Mrs. Hudson. As he got to the living room, he noticed the lights were still on, but there was no sign of Sherlock. Must have sulked into his room.

Thinking nothing of it, John turned the lights off and retired to his own room for the night.

However, what John had failed to notice was the smashed mug, faint smell of chloroform and spots of blood near Sherlock's chair.

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><p><strong>Dun dun DUN. What's gonna happen? Where's Sherlock?<strong>

**Well you'll just have to follow and review to find out ;) Nah, I'm not that horrible, but a follower or two would be greatly appreciated3**

**I'm in the middle of writing the next chapter, so don't worry peeps, it'll be up soon and you won't have to keep rocking back and forth in the isolation of your room thinking about it...well that's what I vision you're doing [Don't ruin my fantasy!]**

**Hope you guys liked it. Oh, and thanks to my lovely beta and best friend Turnedtosteel [check her out, she does AMAZING PWP'S] for beta-ing the last chapter and the others to come :3**


	3. Chapter 3

CH 3/10

The next morning, John woke up late. He leaped out of bed and into the shower. Five minutes later, he was running blindly up to his bedroom, rubbing his hair vigorously with a towel.  
>Within fifteen minutes, John was waving for a cab to take him to work, not even noticing the absence of a particular dark haired detective. He was too much in thought to notice.<p>

The night before, John had woken from one of the weirdest and scariest dreams of his life, and he had PTSD.

_John was standing in a small room, it was so dark you couldn't see the corners of the place. There was a tiny shed of light coming from somewhere, and what it illuminated made John's blood run cold._

_There was Sherlock, tied down to a rusty chair with something metal covering his dark curls. John had no idea what it was but he knew it was important. He looked pale, and obviously dehydrated; the ropes binding his wrists had rubbed his skin raw, but the weird thing to John was that it felt…real. Really real._

_The moment Sherlock raised his head to reveal two perfectly white irises that stared directly at the doctor, John startled awake with his friend's haunting voice in his head._

"_I need your help, John"_

Those words were circling in John's head for the entire morning as he worked. By his lunch break, John was irrationally worried about his friend.

He grabbed a cheap coffee from the cafeteria and headed outside to give Sherlock a call. With every ring, John got more and more worried, although he knew if Sherlock was still in a strop, he wouldn't pick up. But when it went to answer phone three times, John immediately rang Greg. The phone picked up after two rings.

"John? Everything okay?"

"Please tell me Sherlock is with you"

"No" Greg's voice grew worried, "I haven't seen or heard from him since the raid yesterday, why?"

John ran a hand through his sandy hair, sighing "I haven't seen him since I left for a walk and met you"

"You mean you didn't see him when you came home?"

"No. I just thought he was in his bedroom. The lights were still on"

Greg didn't answer for a moment, "Are you at work?"

"Yeah"

"Meet me at Baker Street in half an hour"

John nodded, then realised he was on the phone, "Okay".

John went back up to his office, grabbing his coat and giving some stupid excuse as to why he needed to go, which Sarah didn't believe for a second but let him go nonetheless.

He rushed without realizing. He knew he was being over-paranoid, besides, it was only a dream, he often dreamt of Sherloc-

_No._ _Stop it_, John told himself, for Christ's sake, he was a 40 year old former army doctor, not a teenager with a crush.

He got back to Baker Street in roughly ten minutes, which gave him time to check if Sherlock was actually there to save himself some embarrassment.  
>A quick look around the flat confirmed John's paranoia. His flatmate was nowhere to been seen. It was obvious Sherlock hadn't been in his bedroom recently, his bed was untouched and unslept in.<p>

John ran his hands through his hair, spinning in growing panic in the living room.

"Where are you, Sherlock?" He muttered.

"John?" The doctor heard the Inspector call from the bottom of the stairs.

"Sherlock's not here" John called down from the doorway and Lestrade, Donovan and Anderson arrived in the landing. John narrowed his eyes at the sight of the latter two, but he had more important things to do than start an argument.

Greg looked at John, then nodded to the others to begin searching for any evidence.  
>When Anderson and Donovan were deep into their search, John moved subtly closer to Lestrade.<p>

"Let me guess, they 'volunteered'" he muttered under his breath as Greg nodded, his arms folded as he watch Donovan inspect Sherlock's chair.

"Here" She spoke up, looking intently at her raised, gloved finger.

"What is it?" John approached, eager to find any evidence.

Donovan turned around and showed John a little red dot on her finger, which was otherwise camouflaged by the dark leather of the chair. "It seems the heartless robot can bleed after all"

John bit his tongue. Hard. She only wanted a raise out of him, one that the doctor refused to give her.

"Send it to the lab, check if it's Sherlock's"

"His blood type is B+" John said, then frowned when the others did. "What?" He said defensively, "I had to give him blood once"

After a few moments of silence, Greg cleared his throat, "Well, saying that is Sherlock's blood. Let's see what else we have: an obvious tea pot tip, um, Sherlock's a lot better at this, scuff marks on the carpet and the blood spots…" John looked at Greg, silently begging him not to continue, Greg replied with a silent apology, "It's quite obvious there was a struggle here and we have a kidnapping case on our hands"

Greg's words hung heavily in the air, no one wanting to agree or disagree with the Inspector.

"Right, well" Donovan clapped her hands, her voice echoing, "Better get looking for him, then" She said, like she was talking about the weather, moving to the door, "It's nice to be rid of the freak for 2 seconds but I suppose it's our job to loo- oof!"

John snapped and, within seconds, he had the Sergeant pinned against the wall. "Listen here" He said in a dangerously low voice, "I have had enough with you. Now, it's against my morals to ever hit a woman, but with your so called 'powers': your fucking little super growing cat nails, I'm sure you could hold your own. But the next time you insult Sherlock in the way you just did, don't think for one. Single. Second I won't hesitate in wiping that stupid smirk off your face. And I don't even care about the consequences."

Donovan was speechless to say the least. When John finally eased up –with the help from Greg- Sally almost threw herself out of the door. When John could no longer see her, he managed to calm down.  
>He took a deep breath and turned to the two speechless men, "Sorry about that"<p>

Greg nodded, patting John on the shoulder. "You coming to the station with us? Or do you want to stay here?"

John shook his head, "I'll come, I need him found as quickly as possible, but I'll follow behind in a cab"

"As long as you'll be okay-"

"I'll be okay when Sherlock is found, Greg" John snapped, then calmed down again, "But I am able to keep it together, that's the best I can do at the moment"

Greg sighed, "Alright, mate. We'll meet you at the Yard" he said, and headed for the stairs.

Anderson, who had stayed very silent the entire time –Something John was grateful for- passed him and gave John a sad smile, "We'll find him" He said before exiting, leaving John alone.

"I know" John sighed to himself, looking around the apartment.

Slowly, he walked towards the coat hanger by the door, only now realizing the blue coat and scarf belonging to his missing friend were still there. Feeling sentimental, John reached out and grabbed the scarf, running it through his fingers for a moment before moving it to his face, inhaling the musky scent of the detective.

Soon, John snapped back to reality and, without thinking, pushed the blue material into his coat pocket, before leaving the flat.

**A/N Whoop whoop, 3 down, 7 to go. Already half way through writing the fourth chapter. So yay ^.^ **

**Hope you are enjoying it right now, feel free to leave comments and constructive criticism if you think it's shit ;)**

**Chapter 4 will be up soon, so stay posted **

**Also, sorry about the Donovan slamming. I really do not like how that girl disrespects Sherlock (even though Sherlock isn't exactly innocent). She's a tad OOC in this, sowwy! And I kinda like Anderson, and I think he would treat the situation with seriousness –his actions in Season 3 showed that much-.**

**So, yeah, sorry to anyone who likes Donovan. She won't be a big part in the rest of the fic, so don't worry.**


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